Contacts of the strand formed by residues 234 - 241 (chain A) in PDB entry 6Q2J
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ARG* 2.5 50.8 + - + +
218A ALA 3.6 16.2 - - - +
219A SER* 4.8 2.7 - - - +
232A PRO* 3.2 12.9 - - - +
233A ARG* 1.3 82.5 - - + +
235A VAL* 1.3 62.5 + - - +
236A GLN* 4.1 9.3 + - - +
140C GLY* 5.5 3.8 - - - +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A VAL 3.7 1.2 - - - +
217A ARG* 3.6 3.1 - - - +
218A ALA* 2.9 41.6 + - + +
219A SER 5.4 0.7 - - - -
220A LEU* 4.0 27.1 - - + -
223A LEU* 4.8 15.3 - - + -
225A TRP* 5.6 4.3 - - + -
232A PRO* 4.0 16.2 - - + +
234A GLU* 1.3 76.9 - - - +
236A GLN* 1.3 66.0 + - - +
237A VAL* 3.7 21.2 + - + +
282A MET* 3.8 25.6 - - + -
284A LEU* 6.3 2.2 - - + -
300A LEU* 5.2 4.3 - - + -
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Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A THR* 3.4 26.0 - - + +
216A VAL 3.8 1.6 - - - -
217A ARG* 3.4 40.5 - - - +
234A GLU* 4.1 10.6 + - - +
235A VAL* 1.3 76.7 - - - +
237A VAL* 1.3 60.8 + - - +
238A THR* 5.2 2.7 - - + +
282A MET* 4.7 5.3 - - - +
301A LEU* 3.7 17.7 - - - +
142C VAL* 4.5 24.0 - - + -
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A HIS 3.5 0.9 - - - +
215A THR* 3.3 3.3 - - - -
216A VAL* 2.9 42.3 + - - +
218A ALA* 5.4 4.3 - - + -
223A LEU* 5.5 2.7 - - + -
235A VAL* 3.7 24.0 - - + +
236A GLN* 1.3 75.7 - - - +
238A THR* 1.3 69.4 + - - +
239A MET* 3.7 26.4 + - + +
300A LEU* 4.5 10.8 - - + +
301A LEU* 3.7 12.1 - - + -
254B HIS* 4.5 4.9 - - + -
257B ILE* 4.3 24.2 - - + -
261B LEU* 4.8 6.5 - - + -
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Residues in contact with THR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 4.5 16.6 - - + -
214A HIS 3.3 7.0 - - - -
215A THR* 4.1 16.8 - - + +
236A GLN* 5.2 2.2 - - + +
237A VAL* 1.3 75.7 - - - +
239A MET* 1.3 59.4 + - - +
301A LEU* 3.5 19.7 - - + +
302A ALA* 2.7 49.5 + - - +
254B HIS* 3.6 7.3 - - - -
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Residues in contact with MET 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 3.7 0.7 - - - -
214A HIS* 2.8 34.6 + - - +
216A VAL* 4.3 20.6 - - + -
237A VAL* 3.7 20.6 + - + +
238A THR* 1.3 73.7 - - - +
240A CYS* 1.3 67.9 + - - +
241A ILE* 4.7 8.3 - - + -
302A ALA* 4.6 1.6 - - - -
254B HIS* 3.7 22.2 - - + +
257B ILE* 5.0 2.7 - - + -
258B LYS* 4.9 11.0 - - - -
261B LEU* 3.7 30.5 - - + -
269B VAL* 3.6 39.7 - - + -
270B PRO* 5.1 4.5 - - - -
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Residues in contact with CYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ARG 3.5 17.3 - - - +
213A LEU* 4.0 15.5 - - - -
239A MET* 1.3 83.5 - - - +
241A ILE* 1.3 64.4 + - - +
274A CYS* 3.7 19.3 - - - +
276A PRO* 5.4 2.6 - - + +
302A ALA* 4.7 2.9 - - - -
305A CYS* 2.0 52.9 - - + -
254B HIS* 5.2 1.0 + - - -
258B LYS* 4.4 11.5 + - - +
270B PRO* 4.2 13.9 - - - +
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A CYS 3.4 15.6 - - - +
211A CYS* 4.3 2.3 - - - -
212A ARG 3.7 5.1 + - - +
214A HIS* 3.5 52.2 + - + +
216A VAL* 4.6 10.1 - - + -
239A MET* 4.7 8.1 - - + -
240A CYS* 1.3 79.0 - - - +
242A GLY* 1.3 64.2 + - - +
274A CYS* 5.2 2.2 - - - -
267B ASP 6.1 0.2 - - - +
268B THR* 3.6 43.1 - - + +
270B PRO* 4.4 14.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il